dbSNP rs57744451: PADI4:c.340+97T>C (chr1-17334106-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012387.3(PADI4):c.340+97T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 781,334 control chromosomes in the GnomAD database, including 1,371 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.042 ( 194 hom., cov: 31)

Exomes 𝑓: 0.057 ( 1177 hom. )

Consequence

PADI4
NM_012387.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.407

Publications

4 publications found

Variant links:

Genes affected

PADI4 (HGNC:18368): (peptidyl arginine deiminase 4) This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine residues to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response. [provided by RefSeq, Jul 2008]

PADI4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3 link	c.340+97T>C		intron_variant	Intron 3 of 15	ENST00000375448.4	NP_036519.2	Q9UM07

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4 link	c.340+97T>C		intron_variant	Intron 3 of 15	1	NM_012387.3	ENSP00000364597.4		Q9UM07
PADI4	ENST00000375453.5 link	c.340+97T>C		intron_variant	Intron 3 of 3	2		ENSP00000364602.1		B1AQ67

Frequencies

GnomAD3 genomes

AF:

0.0418

AC:

6355

AN:

152118

Hom.:

189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0106

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0305

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.0822

Gnomad FIN

AF:

0.0531

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0547

Gnomad OTH

AF:

0.0460

GnomAD4 exome

AF:

0.0569

AC:

35778

AN:

629098

Hom.:

1177

AF XY:

0.0593

AC XY:

20043

AN XY:

337872

show subpopulations

African (AFR)

AF:

0.0102

AC:

171

AN:

16776

American (AMR)

AF:

0.0262

AC:

906

AN:

34532

Ashkenazi Jewish (ASJ)

AF:

0.0218

AC:

400

AN:

18378

East Asian (EAS)

AF:

0.0945

AC:

3270

AN:

34610

South Asian (SAS)

AF:

0.0864

AC:

5573

AN:

64490

European-Finnish (FIN)

AF:

0.0536

AC:

2697

AN:

50326

Middle Eastern (MID)

AF:

0.0357

AC:

145

AN:

4066

European-Non Finnish (NFE)

AF:

0.0560

AC:

20901

AN:

373468

Other (OTH)

AF:

0.0528

AC:

1715

AN:

32452

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

1605

3211

4816

6422

8027

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

284

568

852

1136

1420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0419

AC:

6374

AN:

152236

Hom.:

194

Cov.:

AF XY:

0.0425

AC XY:

3167

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0106

AC:

439

AN:

41544

American (AMR)

AF:

0.0305

AC:

466

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0239

AC:

AN:

3472

East Asian (EAS)

AF:

0.104

AC:

540

AN:

5172

South Asian (SAS)

AF:

0.0840

AC:

405

AN:

4824

European-Finnish (FIN)

AF:

0.0531

AC:

563

AN:

10608

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0547

AC:

3721

AN:

68016

Other (OTH)

AF:

0.0502

AC:

106

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

310

619

929

1238

1548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

252

336

420

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0500

Hom.:

Bravo

AF:

0.0376

Asia WGS

AF:

0.104

AC:

362

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.7

(source)

DANN

Benign

0.62

PhyloP100

0.41

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over